Antimicrobial resistance (AMR) is emerging as a potential threat to many lives worldwide. It
is very important to understand and apply effective strategies to counter the impact of AMR …

Some bacteria can transfer to new host species, and this poses a risk to human health.
Indeed, an estimated 60% of all human pathogens have originated from other animal …

Population-level comparisons of prokaryotic genomes must take into account the substantial
differences in gene content resulting from horizontal gene transfer, gene duplication and …

Genome-wide association studies (GWAS) have become indispensable in human medicine
and genomics, but very few have been carried out on bacteria. Here we introduce Scoary …

Fully exploiting the wealth of data in current bacterial population genomics datasets requires
synthesizing and integrating different types of analysis across millions of base pairs in …

The routine use of genomics for disease surveillance provides the opportunity for high-
resolution bacterial epidemiology. Current whole-genome clustering and multilocus ty** …

Disease resistance (R) genes from wild relatives could be used to engineer broad-spectrum
resistance in domesticated crops. We combined association genetics with R gene …

We present fastbaps, a fast solution to the genetic clustering problem. Fastbaps rapidly
identifies an approximate fit to a Dirichlet process mixture model (DPM) for clustering …

Genome-wide association studies (GWAS) in microbes have different challenges to GWAS
in eukaryotes. These have been addressed by a number of different methods. pyseer brings …

The reduced costs of sequencing have led to whole-genome sequences for a large number
of microorganisms, enabling the application of microbial genome-wide association studies …